The Saltdogs claimed their first-ever league title in 2009, winning the American Association Championship. Their overall regular-season record was 49-47, but Lincoln went 27-21 to claim the second-half North Division title, and advanced to the championship by defeating the first-half North champ
Wichita Wingnuts in the division series, three games to two. The Saltdogs then claimed the title by defeating the South Division champion
Pensacola Pelicans three games to two, with Game Five decided by a 2-1 score at Pelican Park in Pensacola.

Lincoln celebrated Season Ten of Saltdogs baseball in 2010, and the team responded with its fourth berth in the playoffs over the past five seasons. The Saltdogs finished with a 51-45 overall record, the seventh time in ten years Lincoln reached the 50-win plateau, and the ninth time in ten seasons that the team finished above the .500 mark. Although the Saltdogs did not win a division title in 2010, their overall record was still good enough for them to qualify for the postseason via a wild card berth. Lincoln has earned four wild-card playoff berths in its history, with the first three (2001, 2002, 2005) coming during the team's Northern League days.

The Saltdogs made the playoffs in each of their first two years in the American Association. In both 2006 and 2007, they finished with the league's best overall regular-season record, winning three of the four North Division titles (both the 1st-half and 2nd-half titles in 2006, and the 1st-half title in 2007). Their 14-game winning streak in 2007 is the longest in team history. The Saltdogs have the best overall record (272-204) of any team in the five-year history of the American Association.

Kash Beauchamp was the first manager in Saltdogs history, although his tenure lasted just 42 games into the 2001 season, during which the team went 21-21 (.500). Pitcher
Les Lancaster replaced Beauchamp, guiding Lincoln to playoff berths in both 2001 and 2002. Lancaster served as a player-manager for the first ten days of his managing tenure before moving exclusively to the bench. He posted a regular-season record of 86-53 (.619), and a postseason record of 6-7. After the 2002 season, Lancaster departed and was replaced by former Toronto Blue Jays manager
Tim Johnson. Johnson spent six seasons with the Saltdogs, compiling a 314-252 (.555) regular-season record and a 2-9 postseason record. Lincoln made the playoffs three times under Johnson (2005, 2006, 2007) and won three division championships (American Association 2006 first-half and second-half North Division titles, 2007 first-half North Division title). Johnson resigned as manager at the end of the 2008 season, and was replaced by Marty Scott, who had managed the Triple-A New Orleans Zephyrs during the '08 season. Scott won two championships between 1995 and 2000 as the manager of the
St. Paul Saints, and guided Lincoln to the 2009 championship, his fourth overall as a manager. Over his two seasons in Lincoln, Scott has compiled a 100-92 (.521) regular-season record, and a 6-7 postseason record.